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- PDB-8izn: Structural study of Interferon-induced, double-stranded RNA-activ... -

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Basic information

Entry
Database: PDB / ID: 8izn
TitleStructural study of Interferon-induced, double-stranded RNA-activated protein kinase (PKR) and Non-structural protein 1 (NS1) complex
Components
  • Interferon-induced, double-stranded RNA-activated protein kinase
  • Non-structural protein 1
KeywordsTRANSFERASE/VIRAL PROTEIN / PKR / NS1 / PKR and NS1 complex / VIRUS / TRANSFERASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / symbiont-mediated suppression of host mRNA processing / response to interferon-alpha / negative regulation of osteoblast proliferation / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / symbiont-mediated suppression of host mRNA processing / response to interferon-alpha / negative regulation of osteoblast proliferation / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell differentiation / regulation of hematopoietic stem cell proliferation / protein serine/threonine kinase inhibitor activity / negative regulation of viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / antiviral innate immune response / cellular response to amino acid starvation / positive regulation of cytokine production / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / response to virus / PKR-mediated signaling / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of non-canonical NF-kappaB signal transduction / double-stranded RNA binding / Interferon alpha/beta signaling / kinase activity / positive regulation of NF-kappaB transcription factor activity / defense response to virus / host cell cytoplasm / protein autophosphorylation / positive regulation of MAPK cascade / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribosome / protein phosphorylation / translation / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / virus-mediated perturbation of host defense response / negative regulation of apoptotic process / host cell nucleus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / S15/NS1, RNA-binding / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase / Non-structural protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.67 Å
AuthorsHan, C.W. / Kim, H.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of PKR and NS1 complex
Authors: Han, C.W.
History
DepositionApr 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-induced, double-stranded RNA-activated protein kinase
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)33,5012
Polymers33,5012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Interferon-induced, double-stranded RNA-activated protein kinase / Eukaryotic translation initiation factor 2-alpha kinase 2 / eIF-2A protein kinase 2 / Interferon- ...Eukaryotic translation initiation factor 2-alpha kinase 2 / eIF-2A protein kinase 2 / Interferon-inducible RNA-dependent protein kinase / P1/eIF-2A protein kinase / Protein kinase RNA-activated / PKR / Protein kinase R / Tyrosine-protein kinase EIF2AK2 / p68 kinase


Mass: 19705.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK2, PKR, PRKR / Production host: Escherichia coli (E. coli)
References: UniProt: P19525, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 13795.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Memphis/102/1972 H3N2)
Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: Q463W9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PKR and NS1 complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 39.99 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49802 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00583767
ELECTRON MICROSCOPYf_angle_d1.90726370
ELECTRON MICROSCOPYf_chiral_restr0.1139354
ELECTRON MICROSCOPYf_plane_restr0.0051588
ELECTRON MICROSCOPYf_dihedral_angle_d9.97821696

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